Re: water models and some questions

Date: Fri May 08 2009 - 09:45:02 CDT

Hi, David:
Thanks for that info, as you sad that SWM4-DP and SWM4-NDP water models are
fully supported, do you have psf, pdb, topology and parameters files for
these models? and are other models like COS-G2/G3 also supported?



On Thu, 7 May 2009 13:54:09 -0500
  David Hardy <> wrote:
> Hi Jose,
> We actually do have support for Drude oscillators in NAMD. We don't yet
>document this capability because we are still missing full support for lone
>pairs required for the force field being developed by Roux and MacKerell.
> The SWM4-DP and SWM4-NDP water models are fully supported.
> The Drude oscillators are integrated using Langevin dynamics
> ("langevin=on") with a two-temperature thermostat that freezes each Drude
>oscillator while keeping its center of mass at room temperature
> ("langevinTemp=300"). The atomic bonds for water need to be kept rigid
>(using Settle). This approach appears to be stable for 1 fs timesteps. The
>two new (and undocumented) configuration file options are "drude=on" and
>"drudeTemp=1" (or however cold you want the oscillators, measured in
>Kelvin). There are enhanced outputs for energy: DRUDECOM and DRUDEBOND
>monitor the two temperatures. There are also DRCOMAVG and DRBONDAVG that
>average over the previous steps, analogous to the TEMPAVG averaging for
>TEMP. You'll see that TEMP (and TEMPAVG) will be much lower than the
>langevinTemp since these measures combine the hot and cold degrees of
>freedom together.
> The PSF needs to be augmented to include the Drude particles and lone
> pairs. This includes the NATOM and NBOND sections. There is also a NUMLP
>section for lone pairs that is not yet supported by NAMD. The new
>interaction parameters can be read in from an additional force field
>parameters file.
> I don't know about the general availability of structure building tools and
>force field parameter files for Drude. Maybe someone else on this list
>knows? We don't yet have support in psfgen for building a Drude PSF.
> Best regards,
> Dave
> On May 7, 2009, at 11:57 AM, Peter Freddolino wrote:
>> Hi Jose,
>> wrote:
>>> Dear namd developers:
>>> I am trying to implement different waters models in Namd,therefore I
>>> have some questions:
>>> 1. In Namd 2.7b1, what does exactly the command "waterModel tip4" do?
>> It turns on a section of the code that enforces the constraint on the
>> position of the TIP4 lone pair, along with making appropriate
>> corrections to the virial.It also changes how namd integrates the
>> motion
>> of massless particles(rather than just giving them a mass of 0.001, as
>> is done in the normal case).
>>> 2. How Does NAMD recognize the hydrogen atoms? I have the feeling
>>> that
>>> is just a mass criteria, so if I have an atom with mass lower than
>>> 1 amu
>>> is going to be considered as a hydrogen atom? All of this is
>>> because I
>>> want to implement some water models with the drude oscillator model.
>> Anything with a mass on the open interval (1.0, 3.5) is considered a
>> hydrogen, anything with a mass on (0.05, 1.0] is a drude, and anything
>> on [0.0,0.05] is a lone pair -- you can find the relevant
>> classification
>> in Molecule.C. There is already a drude model currently being adapted
>> for use in namd; try grepping the code for SWM4. Dave Hardy, who is
>> working on that code, may have additional comments.
>> Best,
>> Peter
>>> Best
>>> Jose Antonio
> --
> David J. Hardy, Ph.D.
> Theoretical and Computational Biophysics
> Beckman Institute, University of Illinois

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